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extract-reads: Extract reads from referenceΒΆ

Docstring:

Usage: qiime feature-classifier extract-reads [OPTIONS]

  Extract sequencing-like reads from a reference database.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                                                                    [required]
Parameters:
  --p-f-primer TEXT       forward primer sequence                   [required]
  --p-r-primer TEXT       reverse primer sequence                   [required]
  --p-trunc-len INTEGER   read is cut to trunc-len if trunc-len is positive.
                          Applied before trim-left.               [default: 0]
  --p-trim-left INTEGER   trim-left nucleotides are removed from the 5' end
                          if trim-left is positive. Applied after trunc-len.
                                                                  [default: 0]
  --p-identity NUMBER     minimum combined primer match identity threshold.
                                                                [default: 0.8]
  --p-min-length INTEGER  Minimum amplicon length. Shorter amplicons are
    Range(0, None)        discarded. Applied after trimming and truncation, so
                          be aware that trimming may impact sequence
                          retention. Set to zero to disable min length
                          filtering.                             [default: 50]
  --p-max-length INTEGER  Maximum amplicon length. Longer amplicons are
    Range(0, None)        discarded. Applied before trimming and truncation,
                          so plan accordingly. Set to zero (default) to
                          disable max length filtering.           [default: 0]
Outputs:
  --o-reads ARTIFACT FeatureData[Sequence]
                                                                    [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.feature_classifier.methods import extract_reads

Docstring:

Extract reads from reference

Extract sequencing-like reads from a reference database.

Parameters
----------
sequences : FeatureData[Sequence]
f_primer : Str
    forward primer sequence
r_primer : Str
    reverse primer sequence
trunc_len : Int, optional
    read is cut to trunc_len if trunc_len is positive. Applied before
    trim_left.
trim_left : Int, optional
    trim_left nucleotides are removed from the 5' end if trim_left is
    positive. Applied after trunc_len.
identity : Float, optional
    minimum combined primer match identity threshold.
min_length : Int % Range(0, None), optional
    Minimum amplicon length. Shorter amplicons are discarded. Applied after
    trimming and truncation, so be aware that trimming may impact sequence
    retention. Set to zero to disable min length filtering.
max_length : Int % Range(0, None), optional
    Maximum amplicon length. Longer amplicons are discarded. Applied before
    trimming and truncation, so plan accordingly. Set to zero (default) to
    disable max length filtering.

Returns
-------
reads : FeatureData[Sequence]